diff --git a/README.md b/README.md new file mode 100644 index 0000000..3e172f6 --- /dev/null +++ b/README.md @@ -0,0 +1,79 @@ +# Striatum Model from Humphries, Wood and Gurney (2010) PLoS Comp Biol + +This is a complete set of code required to run and analyse the striatum model from Humphries, Wood and Gurney (2010) *PLoS Computational Biology*. The code is freely available for study and modification. Please cite the original sources. For questions and assistance contact: +m.d.humphries@shef.ac.uk or drmdhumphries@gmail.com + +--- + +## Top-level Files + +- **Experiment_RandomInput.m:** + The top-level function that runs the model for the results in Fig 9 of the paper; this contains a selection of frequently changed parameters. Extensions to the model should be based on this file. + +- **Experiment_ImpactOnCentreMSN.m:** + The top-level function that runs the model for the results in Fig 10 of the paper; extended to include stimulation of a sub-set of MSNs and FSIs residing a specified spherical shell a set distance from the selected target MSN. This needs to load a 1mm³ network, with 1% FSIs, to run the experiments. This 129MB file `.mat` is available from: + [http://www.abrg.group.shef.ac.uk/code/Striatum/Striatum_network_1000-1000-1000_num_1_at_734299.3923.mat](http://www.abrg.group.shef.ac.uk/code/Striatum/Striatum_network_1000-1000-1000_num_1_at_734299.3923.mat) + +- **StriatumNetworkParameters.m:** + The complete specification of the model; a few of the parameters set here are overwritten in `Experiment_RandomInput.m` or `Experiment_ImpactOnCentreMSN.m`. + +- **RunSimulation.m:** + Function called by `Experiment_RandomInput.m` (or `Experiment_ImpactOnCentreMSN.m`) to handle passing the parameters to the MEX file that runs model simulation. + +- **checkStriatumInputs.m:** + Ensures that all parameters are of the right class and type for handing to the MEX function (called by `RunSimulation.m`). + +--- + +## ./CreateNetwork (folder) + +- **BuildStriatumNetwork.m:** + Builds the network model according to the specified parameters (called by `StriatumNetworkParameters.m`); uses the probability of intersection functions supplied by the 4 `.mat` files in this folder. + +- **GetNeuronPositions.m:** + Puts all neurons in their 3D positions, ensuring that none are closer than the minimum set distance (called by `BuildStriatumNetwork.m`). + +--- + +## ./Simulation (folder) + +This contains the MEX files and source C code for the simulation engines that run the model. The simulation uses the `striatum_RK2` MEX file, solving the ODEs using the midpoint method (aka 2nd order Runge-Kutta). + +The RK2 method MEX files are provided compiled for 32-bit (`.mexw32`) and 64-bit (`.mexw64`) Windows, and for 64-bit (`.mexa64`) Linux systems. We strongly recommend that you recompile the MEX code from the source C++ for your platform. + +--- + +## ./Analyses (folder) + +- **firing_stats_solo.m:** + Analyses of the firing properties of a simulation, including firing rate distributions. + +- **analyse_centre_MSN.m:** + Impact of inputs on centre MSN. + +- **raster_plot.m:** + Helper function for the analyses. Plots rasters of spike-train data. + +--- + +## Notes + +1. This code represents version 1.5 of our striatal model: it combines the new 3D connectivity model with the neuron and gap junction models from version 1 (published in Humphries et al, 2009; ModelDB ID:128874). + +2. This code does not include our updated model of dopamine's effects on the MSN (Humphries, Lepora, Wood & Gurney, 2009b). + +--- + +## References + +Humphries, M. D., Wood, R. & Gurney, K. (2009) Dopamine-modulated dynamic cell assemblies generated by the GABAergic striatal microcircuit. *Neural Networks*, 22, 1174-1188. Download at: +[http://dx.doi.org/10.1016/j.neunet.2009.07.018](http://dx.doi.org/10.1016/j.neunet.2009.07.018) + +Humphries, M. D.; Lepora, N.; Wood, R. & Gurney, K. (2009b) Capturing dopaminergic modulation and bimodal membrane behaviour of striatal medium spiny neurons in accurate, reduced models. *Frontiers in Computational Neuroscience*, 3, 26. Download at: +[http://dx.doi.org/10.3389/neuro.10.026.2009](http://dx.doi.org/10.3389/neuro.10.026.2009) + +Humphries, M. D., Wood, R. & Gurney, K. (2010) Reconstructing the three-dimensional GABAergic microcircuit of the striatum. *PLoS Computational Biology*, 6, e100101. [PDF copy included] + +--- + +2025-06-20: Converted README to Markdown. \ No newline at end of file diff --git a/README.txt b/README.txt deleted file mode 100644 index 8fe3987..0000000 --- a/README.txt +++ /dev/null @@ -1,102 +0,0 @@ -This is a complete set of code required to run and analyse the -striatum model from Humphries, Wood and Gurney (2010) PLoS Comp Biol. -The code is freely available for study and modification. Please -cite the original sources. For questions and assistance contact: -m.d.humphries@shef.ac.uk or drmdhumphries@gmail.com - -************************************************************************ - -Top-level Files: - -Experiment_RandomInput.m: the top-level function that runs the model - for the results in Fig 9 of the paper; this - contains a selection of frequently changed - parameters. Extensions to the model should - be based on this file - -Experiment_ImpactOnCentreMSN.m: the top-level function that runs the - model for the results in Fig 10 of the - paper; extended to include stimulation of a - sub-set of MSNs and FSIs residing a - specified spherical shell a set distance - from the selected target MSN. This needs to - load a 1mm3 network, with 1% FSIs, to run - the experiments. This 129MB file .mat is - available from: -http://www.abrg.group.shef.ac.uk/code/Striatum/Striatum_network_1000-1000-1000_num_1_at_734299.3923.mat - -StriatumNetworkParameters.m: the complete specification of the model; - a few of the parameters set here are - overwritten in - Experiment_RandomInput.m or - Experiment_ImpactOnCentreMSN.m - RunSimulation.m: function called by - Experiment_RandomInput.m (or - Experiment_ImpactOnCentreMSN.m) to - handle passing the parameters to the - MEX file that runs model simulation - checkStriatumInputs.m: ensures that - all parameters are of the right class - and type for handing to the MEX - function (called by RunSimulation.m) - -./CreateNetwork (folder): -BuildStriatumNetwork.m: builds the network model according to the - specified parameters (called by - StriatumNetworkParameters.m); uses the - probability of intersection functions supplied - by the 4 .mat files in this folder - GetNeuronPositions.m: puts all neurons in - their 3D positions, ensuring that none are - closer than the minimum set distance (called - by BuildStriatumNetwork.m) - -./Simulation (folder): -This contains the MEX files and source C code for the simulation -engines that run the model. The simulation uses the striatum_RK2 MEX -file, solving the ODEs using the midpoint method (aka 2nd order -Runge-Kutta). - -The RK2 method MEX files are provided compiled for 32-bit (.mexw32) -and 64-bit (.mexw64) Windows, and for 64-bit (.mexa64) Linux -systems. We strongly recommend that you recompile the MEX code from -the source C++ for your platform - -./Analyses (folder): -firing_stats_solo.m: analyses of the firing properties of a -simulation, including firing rate distributions analyse_centre_MSN.m: -impact of inputs on centre MSN raster_plot.m: helper function for the -analyses. Plots rasters of spike-train data. - -********************************************************************** - -Notes: - -(1) This code represents version 1.5 of our striatal model: it -combines the new 3D connectivity model with the neuron and gap -junction models from version 1 (published in Humphries et al, 2009; -ModelDB ID:128874) - -(2) This code does not include our updated model of dopamine's effects -on the MSN (Humphries, Lepora, Wood & Gurney, 2009b) - - - -*********************************************************************** -References: - -Humphries, M. D., Wood, R. & Gurney, K. (2009) Dopamine-modulated -dynamic cell assemblies generated by the GABAergic striatal -microcircuit Neural Networks,22, 1174-1188. Download at: -http://dx.doi.org/10.1016/j.neunet.2009.07.018 - -Humphries, M. D.; Lepora, N.; Wood, R. & Gurney, K. (2009b) Capturing -dopaminergic modulation and bimodal membrane behaviour of striatal -medium spiny neurons in accurate, reduced models. Frontiers in -Computational Neuroscience, 3, 26. Download at: -http://dx.doi.org/10.3389/neuro.10.026.2009 - -Humphries, M. D., Wood, R. & Gurney, K. (2010) Reconstructing the -three-dimensional GABAergic microcircuit of the striatum. PLoS -Computational Biology, 6, e100101. [PDF copy included] -